View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector FEBS Letters 583 (2009) 3455–3460 journal homepage: www.FEBSLetters.org Translation termination in pyrrolysine-utilizing archaea Elena Alkalaeva a, Boris Eliseev a, Alexandre Ambrogelly c, Peter Vlasov a, Fyodor A. Kondrashov b, Sharath Gundllapalli c, Lyudmila Frolova a,*, Dieter Söll c,d, Lev Kisselev a,1 a Engelhardt Institute of Molecular Biology, the Russian Academy of Sciences, Vavilov str. 32, Moscow 119991, Russia b Bioinformatics and Genomics Programme, Centre for Genomic Regulation, 08003 Barcelona, Spain c Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8114, USA d Department of Chemistry, Yale University, New Haven, CT 06520-8114, USA article info abstract Article history: Although some data link archaeal and eukaryotic translation, the overall mechanism of protein syn- Received 28 August 2009 thesis in archaea remains largely obscure. Both archaeal (aRF1) and eukaryotic (eRF1) single release Accepted 24 September 2009 factors recognize all three stop codons. The archaeal genus Methanosarcinaceae contains two aRF1 Available online 29 September 2009 homologs, and also uses the UAG stop to encode the 22nd amino acid, pyrrolysine. Here we provide an analysis of the last stage of archaeal translation in pyrrolysine-utilizing species. We demon- Edited by Michael Ibba strated that only one of two Methanosarcina barkeri aRF1 homologs possesses activity and recog- In memory of Lev Kisselev nizes all three stop codons. The second aRF1 homolog may have another unknown function. The mechanism of pyrrolysine incorporation in the Methanosarcinaceae is discussed. Keywords: Ó 2009 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. Translation termination Archeon Pyrrolysine-utilizing archea aRF1 Polypeptide release factor 1. Introduction while the other Pyl-containing archaea, Methanosarcina mazei and Methanococcoides burtonii, have only one aRF1 [5]. At the final stage of protein biosynthesis the class-1 release fac- An in-frame UAG codon has been identified in mtmB1 encoding tors (RF1s) recognize stop codons and induce hydrolysis of pepti- MtmB1, a methylamine methyltransferase participating in metha- dyl-tRNA in the peptidyl transferase center of the ribosome nogenesis from monomethylamine in M. barkeri (reviewed in [6]). (reviewed in [1–3]). In eukaryotes a single release factor (eRF1) The UAG is translated by the novel amino acid Pyl as revealed by recognizes all three stop codons, UAA, UAG and UGA. Bacteria have the crystal structure of MtmB1 [7]. An in-frame UAG codon is also two release factors (RF1 and RF2) that recognize different stop-co- contained in mtbB1 and mttB1, the genes encoding the di- and tri- don pairs, UAA/UAG and UAA/UGA, respectively. Archaeal class-1 methylamine methyltransferases in Methanosarcina spp. (reviewed release factors (aRF1s) exhibit a high degree of amino acid se- in [6]), as well as in a number of other open reading frames [8,9]. quence similarity with eRF1s and are substantially different from Examination of the presently sequenced genomes suggests that bacterial RFs (Fig. 1). Like eRF1, aRF1 recognizes all three stop co- the existence of Pyl is limited to the Methanosarcinaceae (Methan- dons [4], demonstrating the functional resemblance of aRF1 and osarcina spp. and M. burtonii) and to a few bacteria (Desulfitobacte- eRF1. Thus, archaeal translation termination has common features rium hafniense [10] and symbiotic d-proteobacteria [9,11]). with eukaryotic termination and their mechanisms are expected to Pyl is co-translationally inserted at UAG codons and as such be similar. Most archaea contain only one gene encoding aRF1, but constitutes the 22nd natural amino acid used in protein synthesis. in two species of pyrrolysine (Pyl)-utilizing archaea, Methanosarci- Pyl has its own tRNAPyl whose CUA anticodon complements the na barkeri and Methanosarcina acetivorans, two non-identical class- UAG codon [10], and a special aminoacyl-tRNA synthetase (PylRS) 1 translation termination factors were found (aRF1-1 and aRF1-2), that specifically acylates tRNAPyl to form Pyl-tRNAPyl [12,13]. While the molecular principles governing the synthesis of Pyl-tRNAPyl have been worked out in details, the mechanism underlying the recoding of the UGA codon as Pyl sense codon remains poorly * Corresponding author. Fax: +7 (499) 135 14 05. E-mail address: [email protected] (L. Frolova). understood. Pyl share with selenocysteine (Sec) the property of 1 Deceased April 12, 2008. being inserted at in-frame stop codons (UGA for Sec). Selenocys- 0014-5793/$36.00 Ó 2009 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved. doi:10.1016/j.febslet.2009.09.044 3456 E. Alkalaeva et al. / FEBS Letters 583 (2009) 3455–3460 Fig. 1. Multiple sequence alignment of the N-terminal domains of release factors from different archaea, eukaryotes and bacteria. teine incorporation into protein has been thoroughly examined. sites. M. maripaludis aRF1 gene was cloned following the same pro- For Sec, a RNA stem loop (termed SECIS element) located in the cedure and subcloned in pET15b between NdeI and XhoI sites. mRNA signals the UGA codon to be recoded to the translation machinery. In addition, an essential tRNASec-specific elongation 2.2. Chimeric archaeal/human release factor constructs factor (SelB or EFSec) delivers the Sec-tRNASec at the suppression site, ensuring the successful translation of the in-frame UGA codon The aRF1 gene sequences encoding the N domains of M. barkeri as selenocysteine [14–17]. aRF1-1 and aRF1-2 and M. maripaludis aRF1 were PCR-amplified While it was initially thought that Pyl insertion mechanism using specific primers. The first primer contained an NdeI site and could be modeled on that of Sec, recent data suggest otherwise. the second one carried a SalI site in putative boundary of the N and A stem loop structure analogous to the SECIS element (and thus M domains of aRF1 (codons for amino acids 144 and 145, numbered termed PYLIS element) was predicted downstream of the in-frame according to human eRF1). The determination of the putative bound- UAG codon in mtmB1 mRNAs [18,19]. However, in contrast to Sec, aries between the N and M domains of aRF1s was based on the crystal the presence of the RNA stem loop structure was not critical for the structure of human eRF1 [23] and a multiple alignment of protein se- insertion of Pyl into proteins. The PYLIS structure moderately mod- quences of archaeal and human release factors. The resulting PCR ulated MtmB1 expression in Methanosarcina and did not impact re- products were inserted into NdeI/SalI sites of the pERF4b-Sal plasmid. porter protein expression in an Escherichia coli context [20,21]. pERF4b-Sal plasmid with cloned eRF1 gene from Homo sapiens in- Sequence comparison studies showed that PYLIS structure is not serted into SalI restriction site of pET23b(+) vector (Novagen) was conserved in the mtbB1 and mttB1 mRNAs. Lastly, in vitro and constructed previously [24]. Thus, three plasmids carrying chimeric in vivo experiments in E. coli demonstrated that elongation factor genes encoding the archaeal N domain of aRF1s and MC domain of Tu is capable of interacting and delivering Pyl-tRNAPyl to the UGA human eRF1 with 6His-tag on the C-terminus were obtained. Mutant suppression site, suggesting that no specialized elongation factor forms carrying the N domain of M. barkeri aRF1-2 with amino acid is required for Pyl insertion [22]. substitutions corresponding to the amino acid sequence of M. barkeri In order to gain further insight into UAG recoding mechanism, aRF1-1 (K61N or D122V + I124K or D122T + Y123F + I124V; amino we have determined stop codon specificity of two M. barkeri acid numbering according to human eRF1) were obtained by PCR aRF1 homologs in an in vitro reconstituted eukaryotic translation mutagenesis as described [25]. system. For these purposes we constructed chimeric proteins which contain the N-terminal domain of M. barkeri aRF1s (respon- 2.3. Proteins and ribosomal subunits sible for stop-codon decoding) and the MC domains of human eRF1 since the full-length aRF1s from this organism are unable to inter- The 40S and 60S ribosomal subunits, eIF2, eIF3, eIF4F, eEF1H act with eukaryotic ribosomes used in translation termination as- and eEF2 were purified from rabbit reticulocyte lysate as described say. We have shown that only one out of two forms of M. barkeri (see references in [26]). The eukaryotic translation factors eIF1, aRF1s is active in translation termination and recognizes all three eIF1A, eIF4A, eIF4B, eIF5B, eIF5, eRF1, chimeric a/eRF1 were pro- stop codons. Taking into account that the frequency of UAG stop- duced as recombinant proteins in E. coli strain BL21 with subse- codon usage is substantially decreased in Pyl-encoding genomes, quent protein purification on Ni-NTA-agarose and ion-exchange our data suggest that the Methanosarcinaceae may be in a contin- chromatography (see references in [26]). uing process of the UAG codon reassignment from a stop signal to a sense codon specifying Pyl. 2.4. mRNA transcripts 2. Materials and methods mRNA was transcribed by T7 RNA polymerase on MVHL-stop plasmids, encoding T7 promoter, four CAA repeats, b-globin 50- 2.1. M. barkeri and Methanococcus maripaludis aRF1 gene constructs untranslated region (UTR), MVHL tetrapeptide followed by one of three stop codons (UAA, UAG or UGA) and 30-UTR comprising the rest M. barkeri wild-type aRF1-1 and aRF1-2 genes were amplified by of the natural b-globin coding sequence. MVHL-UAA plasmid was de- PCR using freshly prepared genomic DNA. PCR products were scribed [26], and MVHL constructs containing UAG and UGA stop co- cloned in Topo TA (Invitrogen), sequenced and subcloned into dons were obtained by PCR mutagenesis of MVHL-UAA plasmid. For pET15b expression plasmid between BamHI and PstI restriction run-off transcription all plasmids were linearized with XhoI.